Search Results for: label/microbiology

Post navigation

The four basic categories of molecules for building life are carbohydrates, lipids, proteins, and nucleic acids.

Carbohydrates serve many purposes, from energy to structure to chemical communication, as monomers or polymers.

Lipids, which are hydrophobic, also have different purposes, including energy storage, structure, and signaling.

Proteins, made of amino acids in up to four structural levels, are involved in just about every process of life.

The nucleic acids DNA and RNA consist of four nucleotide building blocks, and each has different purposes.

The longer version

Life is so diverse and unwieldy, it may surprise you to learn that we can break it down into four basic categories of molecules. Possibly even more implausible is the fact that two of these categories of large molecules themselves break down into a surprisingly small number of building blocks. The proteins that make up all of the living things on this planet and ensure their appropriate structure and smooth function consist of only 20 different kinds of building blocks. Nucleic acids, specifically DNA, are even more basic: only four different kinds of molecules provide the materials to build the countless different genetic codes that translate into all the different walking, swimming, crawling, oozing, and/or photosynthesizing organisms that populate the third rock from the Sun.

Big Molecules with Small Building Blocks

The functional groups, assembled into building blocks on backbones of carbon atoms, can be bonded together to yield large molecules that we classify into four basic categories. These molecules, in many different permutations, are the basis for the diversity that we see among living things. They can consist of thousands of atoms, but only a handful of different kinds of atoms form them. It’s like building apartment buildings using a small selection of different materials: bricks, mortar, iron, glass, and wood. Arranged in different ways, these few materials can yield a huge variety of structures.

We encountered functional groups and the SPHONC in Chapter 3. These components form the four categories of molecules of life. These Big Four biological molecules are carbohydrates, lipids, proteins, and nucleic acids. They can have many roles, from giving an organism structure to being involved in one of the millions of processes of living. Let’s meet each category individually and discover the basic roles of each in the structure and function of life.

Carbohydrates

You have met carbohydrates before, whether you know it or not. We refer to them casually as “sugars,” molecules made of carbon, hydrogen, and oxygen. A sugar molecule has a carbon backbone, usually five or six carbons in the ones we’ll discuss here, but it can be as few as three. Sugar molecules can link together in pairs or in chains or branching “trees,” either for structure or energy storage.

When you look on a nutrition label, you’ll see reference to “sugars.” That term includes carbohydrates that provide energy, which we get from breaking the chemical bonds in a sugar called glucose. The “sugars” on a nutrition label also include those that give structure to a plant, which we call fiber. Both are important nutrients for people.

Sugars serve many purposes. They give crunch to the cell walls of a plant or the exoskeleton of a beetle and chemical energy to the marathon runner. When attached to other molecules, like proteins or fats, they aid in communication between cells. But before we get any further into their uses, let’s talk structure.

The sugars we encounter most in basic biology have their five or six carbons linked together in a ring. There’s no need to dive deep into organic chemistry, but there are a couple of essential things to know to interpret the standard representations of these molecules.

Check out the sugars depicted in the figure. The top-left molecule, glucose, has six carbons, which have been numbered. The sugar to its right is the same glucose, with all but one “C” removed. The other five carbons are still there but are inferred using the conventions of organic chemistry: Anywhere there is a corner, there’s a carbon unless otherwise indicated. It might be a good exercise for you to add in a “C” over each corner so that you gain a good understanding of this convention. You should end up adding in five carbon symbols; the sixth is already given because that is conventionally included when it occurs outside of the ring.

On the left is a glucose with all of its carbons indicated. They’re also numbered, which is important to understand now for information that comes later. On the right is the same molecule, glucose, without the carbons indicated (except for the sixth one). Wherever there is a corner, there is a carbon, unless otherwise indicated (as with the oxygen). On the bottom left is ribose, the sugar found in RNA. The sugar on the bottom right is deoxyribose. Note that at carbon 2 (*), the ribose and deoxyribose differ by a single oxygen.

The lower left sugar in the figure is a ribose. In this depiction, the carbons, except the one outside of the ring, have not been drawn in, and they are not numbered. This is the standard way sugars are presented in texts. Can you tell how many carbons there are in this sugar? Count the corners and don’t forget the one that’s already indicated!

If you said “five,” you are right. Ribose is a pentose (pent = five) and happens to be the sugar present in ribonucleic acid, or RNA. Think to yourself what the sugar might be in deoxyribonucleic acid, or DNA. If you thought, deoxyribose, you’d be right.

The fourth sugar given in the figure is a deoxyribose. In organic chemistry, it’s not enough to know that corners indicate carbons. Each carbon also has a specific number, which becomes important in discussions of nucleic acids. Luckily, we get to keep our carbon counting pretty simple in basic biology. To count carbons, you start with the carbon to the right of the non-carbon corner of the molecule. The deoxyribose or ribose always looks to me like a little cupcake with a cherry on top. The “cherry” is an oxygen. To the right of that oxygen, we start counting carbons, so that corner to the right of the “cherry” is the first carbon. Now, keep counting. Here’s a little test: What is hanging down from carbon 2 of the deoxyribose?

If you said a hydrogen (H), you are right! Now, compare the deoxyribose to the ribose. Do you see the difference in what hangs off of the carbon 2 of each sugar? You’ll see that the carbon 2 of ribose has an –OH, rather than an H. The reason the deoxyribose is called that is because the O on the second carbon of the ribose has been removed, leaving a “deoxyed” ribose. This tiny distinction between the sugars used in DNA and RNA is significant enough in biology that we use it to distinguish the two nucleic acids.

In fact, these subtle differences in sugars mean big differences for many biological molecules. Below, you’ll find a couple of ways that apparently small changes in a sugar molecule can mean big changes in what it does. These little changes make the difference between a delicious sugar cookie and the crunchy exoskeleton of a dung beetle.

Sugar and Fuel

A marathon runner keeps fuel on hand in the form of “carbs,” or sugars. These fuels provide the marathoner’s straining body with the energy it needs to keep the muscles pumping. When we take in sugar like this, it often comes in the form of glucose molecules attached together in a polymer called starch. We are especially equipped to start breaking off individual glucose molecules the minute we start chewing on a starch.

Double X Extra: A monomer is a building block (mono = one) and a polymer is a chain of monomers. With a few dozen monomers or building blocks, we get millions of different polymers. That may sound nutty until you think of the infinity of values that can be built using only the numbers 0 through 9 as building blocks or the intricate programming that is done using only a binary code of zeros and ones in different combinations.

Our bodies then can rapidly take the single molecules, or monomers, into cells and crack open the chemical bonds to transform the energy for use. The bonds of a sugar are packed with chemical energy that we capture to build a different kind of energy-containing molecule that our muscles access easily. Most species rely on this process of capturing energy from sugars and transforming it for specific purposes.

Polysaccharides: Fuel and Form

Plants use the Sun’s energy to make their own glucose, and starch is actually a plant’s way of storing up that sugar. Potatoes, for example, are quite good at packing away tons of glucose molecules and are known to dieticians as a “starchy” vegetable. The glucose molecules in starch are packed fairly closely together. A string of sugar molecules bonded together through dehydration synthesis, as they are in starch, is a polymer called a polysaccharide (poly = many; saccharide = sugar). When the monomers of the polysaccharide are released, as when our bodies break them up, the reaction that releases them is called hydrolysis.

Double X Extra: The specific reaction that hooks one monomer to another in a covalent bond is called dehydration synthesis because in making the bond–synthesizing the larger molecule–a molecule of water is removed (dehydration). The reverse is hydrolysis (hydro = water; lysis = breaking), which breaks the covalent bond by the addition of a molecule of water.

Although plants make their own glucose and animals acquire it by eating the plants, animals can also package away the glucose they eat for later use. Animals, including humans, store glucose in a polysaccharide called glycogen, which is more branched than starch. In us, we build this energy reserve primarily in the liver and access it when our glucose levels drop.

Whether starch or glycogen, the glucose molecules that are stored are bonded together so that all of the molecules are oriented the same way. If you view the sixth carbon of the glucose to be a “carbon flag,” you’ll see in the figure that all of the glucose molecules in starch are oriented with their carbon flags on the upper left.

The orientation of monomers of glucose in polysaccharides can make a big difference in the use of the polymer. The glucoses in the molecule on the top are all oriented “up” and form starch. The glucoses in the molecule on the bottom alternate orientation to form cellulose, which is quite different in its function from starch.

Storing up sugars for fuel and using them as fuel isn’t the end of the uses of sugar. In fact, sugars serve as structural molecules in a huge variety of organisms, including fungi, bacteria, plants, and insects.

The primary structural role of a sugar is as a component of the cell wall, giving the organism support against gravity. In plants, the familiar old glucose molecule serves as one building block of the plant cell wall, but with a catch: The molecules are oriented in an alternating up-down fashion. The resulting structural sugar is called cellulose.

That simple difference in orientation means the difference between a polysaccharide as fuel for us and a polysaccharide as structure. Insects take it step further with the polysaccharide that makes up their exoskeleton, or outer shell. Once again, the building block is glucose, arranged as it is in cellulose, in an alternating conformation. But in insects, each glucose has a little extra added on, a chemical group called an N-acetyl group. This addition of a single functional group alters the use of cellulose and turns it into a structural molecule that gives bugs that special crunchy sound when you accidentally…ahem…step on them.

These variations on the simple theme of a basic carbon-ring-as-building-block occur again and again in biological systems. In addition to serving roles in structure and as fuel, sugars also play a role in function. The attachment of subtly different sugar molecules to a protein or a lipid is one way cells communicate chemically with one another in refined, regulated interactions. It’s as though the cells talk with each other using a specialized, sugar-based vocabulary. Typically, cells display these sugary messages to the outside world, making them available to other cells that can recognize the molecular language.

Lipids: The Fatty Trifecta

Starch makes for good, accessible fuel, something that we immediately attack chemically and break up for quick energy. But fats are energy that we are supposed to bank away for a good long time and break out in times of deprivation. Like sugars, fats serve several purposes, including as a dense source of energy and as a universal structural component of cell membranes everywhere.

Fats: the Good, the Bad, the Neutral

Turn again to a nutrition label, and you’ll see a few references to fats, also known as lipids. (Fats are slightly less confusing that sugars in that they have only two names.) The label may break down fats into categories, including trans fats, saturated fats, unsaturated fats, and cholesterol. You may have learned that trans fats are “bad” and that there is good cholesterol and bad cholesterol, but what does it all mean?

Let’s start with what we mean when we say saturated fat. The question is, saturated with what? There is a specific kind of dietary fat call the triglyceride. As its name implies, it has a structural motif in which something is repeated three times. That something is a chain of carbons and hydrogens, hanging off in triplicate from a head made of glycerol, as the figure shows. Those three carbon-hydrogen chains, or fatty acids, are the “tri” in a triglyceride. Chains like this can be many carbons long.

Double X Extra: We call a fatty acid a fatty acid because it’s got a carboxylic acid attached to a fatty tail. A triglyceride consists of three of these fatty acids attached to a molecule called glycerol. Our dietary fat primarily consists of these triglycerides.

Triglycerides come in several forms. You may recall that carbon can form several different kinds of bonds, including single bonds, as with hydrogen, and double bonds, as with itself. A chain of carbon and hydrogens can have every single available carbon bond taken by a hydrogen in single covalent bond. This scenario of hydrogen saturation yields a saturated fat. The fat is saturated to its fullest with every covalent bond taken by hydrogens single bonded to the carbons.

Saturated fats have predictable characteristics. They lie flat easily and stick to each other, meaning that at room temperature, they form a dense solid. You will realize this if you find a little bit of fat on you to pinch. Does it feel pretty solid? That’s because animal fat is saturated fat. The fat on a steak is also solid at room temperature, and in fact, it takes a pretty high heat to loosen it up enough to become liquid. Animals are not the only organisms that produce saturated fat–avocados and coconuts also are known for their saturated fat content.

The top graphic above depicts a triglyceride with the glycerol, acid, and three hydrocarbon tails. The tails of this saturated fat, with every possible hydrogen space occupied, lie comparatively flat on one another, and this kind of fat is solid at room temperature. The fat on the bottom, however, is unsaturated, with bends or kinks wherever two carbons have double bonded, booting a couple of hydrogens and making this fat unsaturated, or lacking some hydrogens. Because of the space between the bumps, this fat is probably not solid at room temperature, but liquid.

You can probably now guess what an unsaturated fat is–one that has one or more hydrogens missing. Instead of single bonding with hydrogens at every available space, two or more carbons in an unsaturated fat chain will form a double bond with carbon, leaving no space for a hydrogen. Because some carbons in the chain share two pairs of electrons, they physically draw closer to one another than they do in a single bond. This tighter bonding result in a “kink” in the fatty acid chain.

In a fat with these kinks, the three fatty acids don’t lie as densely packed with each other as they do in a saturated fat. The kinks leave spaces between them. Thus, unsaturated fats are less dense than saturated fats and often will be liquid at room temperature. A good example of a liquid unsaturated fat at room temperature is canola oil.

A few decades ago, food scientists discovered that unsaturated fats could be resaturated or hydrogenated to behave more like saturated fats and have a longer shelf life. The process of hydrogenation–adding in hydrogens–yields trans fat. This kind of processed fat is now frowned upon and is being removed from many foods because of its associations with adverse health effects. If you check a food label and it lists among the ingredients “partially hydrogenated” oils, that can mean that the food contains trans fat.

Double X Extra: A triglyceride can have up to three different fatty acids attached to it. Canola oil, for example, consists primarily of oleic acid, linoleic acid, and linolenic acid, all of which are unsaturated fatty acids with 18 carbons in their chains.

Why do we take in fat anyway? Fat is a necessary nutrient for everything from our nervous systems to our circulatory health. It also, under appropriate conditions, is an excellent way to store up densely packaged energy for the times when stores are running low. We really can’t live very well without it.

Phospholipids: An Abundant Fat

You may have heard that oil and water don’t mix, and indeed, it is something you can observe for yourself. Drop a pat of butter–pure saturated fat–into a bowl of water and watch it just sit there. Even if you try mixing it with a spoon, it will just sit there. Now, drop a spoon of salt into the water and stir it a bit. The salt seems to vanish. You’ve just illustrated the difference between a water-fearing (hydrophobic) and a water-loving (hydrophilic) substance.

Generally speaking, compounds that have an unequal sharing of electrons (like ions or anything with a covalent bond between oxygen and hydrogen or nitrogen and hydrogen) will be hydrophilic. The reason is that a charge or an unequal electron sharing gives the molecule polarity that allows it to interact with water through hydrogen bonds. A fat, however, consists largely of hydrogen and carbon in those long chains. Carbon and hydrogen have roughly equivalent electronegativities, and their electron-sharing relationship is relatively nonpolar. Fat, lacking in polarity, doesn’t interact with water. As the butter demonstrated, it just sits there.

There is one exception to that little maxim about fat and water, and that exception is the phospholipid. This lipid has a special structure that makes it just right for the job it does: forming the membranes of cells. A phospholipid consists of a polar phosphate head–P and O don’t share equally–and a couple of nonpolar hydrocarbon tails, as the figure shows. If you look at the figure, you’ll see that one of the two tails has a little kick in it, thanks to a double bond between the two carbons there.

Phospholipids form a double layer and are the major structural components of cell membranes. Their bend, or kick, in one of the hydrocarbon tails helps ensure fluidity of the cell membrane. The molecules are bipolar, with hydrophilic heads for interacting with the internal and external watery environments of the cell and hydrophobic tails that help cell membranes behave as general security guards.

The kick and the bipolar (hydrophobic and hydrophilic) nature of the phospholipid make it the perfect molecule for building a cell membrane. A cell needs a watery outside to survive. It also needs a watery inside to survive. Thus, it must face the inside and outside worlds with something that interacts well with water. But it also must protect itself against unwanted intruders, providing a barrier that keeps unwanted things out and keeps necessary molecules in.

Phospholipids achieve it all. They assemble into a double layer around a cell but orient to allow interaction with the watery external and internal environments. On the layer facing the inside of the cell, the phospholipids orient their polar, hydrophilic heads to the watery inner environment and their tails away from it. On the layer to the outside of the cell, they do the same.

As the figure shows, the result is a double layer of phospholipids with each layer facing a polar, hydrophilic head to the watery environments. The tails of each layer face one another. They form a hydrophobic, fatty moat around a cell that serves as a general gatekeeper, much in the way that your skin does for you. Charged particles cannot simply slip across this fatty moat because they can’t interact with it. And to keep the fat fluid, one tail of each phospholipid has that little kick, giving the cell membrane a fluid, liquidy flow and keeping it from being solid and unforgiving at temperatures in which cells thrive.

Steroids: Here to Pump You Up?

Our final molecule in the lipid fatty trifecta is cholesterol. As you may have heard, there are a few different kinds of cholesterol, some of which we consider to be “good” and some of which is “bad.” The good cholesterol, high-density lipoprotein, or HDL, in part helps us out because it removes the bad cholesterol, low-density lipoprotein or LDL, from our blood. The presence of LDL is associated with inflammation of the lining of the blood vessels, which can lead to a variety of health problems.

But cholesterol has some other reasons for existing. One of its roles is in the maintenance of cell membrane fluidity. Cholesterol is inserted throughout the lipid bilayer and serves as a block to the fatty tails that might otherwise stick together and become a bit too solid.

Cholesterol’s other starring role as a lipid is as the starting molecule for a class of hormones we called steroids or steroid hormones. With a few snips here and additions there, cholesterol can be changed into the steroid hormones progesterone, testosterone, or estrogen. These molecules look quite similar, but they play very different roles in organisms. Testosterone, for example, generally masculinizes vertebrates (animals with backbones), while progesterone and estrogen play a role in regulating the ovulatory cycle.

Double X Extra: A hormone is a blood-borne signaling molecule. It can be lipid based, like testosterone, or short protein, like insulin.

Proteins

As you progress through learning biology, one thing will become more and more clear: Most cells function primarily as protein factories. It may surprise you to learn that proteins, which we often talk about in terms of food intake, are the fundamental molecule of many of life’s processes. Enzymes, for example, form a single broad category of proteins, but there are millions of them, each one governing a small step in the molecular pathways that are required for living.

Levels of Structure

Amino acids are the building blocks of proteins. A few amino acids strung together is called a peptide, while many many peptides linked together form a polypeptide. When many amino acids strung together interact with each other to form a properly folded molecule, we call that molecule a protein.

For a string of amino acids to ultimately fold up into an active protein, they must first be assembled in the correct order. The code for their assembly lies in the DNA, but once that code has been read and the amino acid chain built, we call that simple, unfolded chain the primary structure of the protein.

This chain can consist of hundreds of amino acids that interact all along the sequence. Some amino acids are hydrophobic and some are hydrophilic. In this context, like interacts best with like, so the hydrophobic amino acids will interact with one another, and the hydrophilic amino acids will interact together. As these contacts occur along the string of molecules, different conformations will arise in different parts of the chain. We call these different conformations along the amino acid chain the protein’s secondary structure.

Once those interactions have occurred, the protein can fold into its final, or tertiary structure and be ready to serve as an active participant in cellular processes. To achieve the tertiary structure, the amino acid chain’s secondary interactions must usually be ongoing, and the pH, temperature, and salt balance must be just right to facilitate the folding. This tertiary folding takes place through interactions of the secondary structures along the different parts of the amino acid chain.

The final product is a properly folded protein. If we could see it with the naked eye, it might look a lot like a wadded up string of pearls, but that “wadded up” look is misleading. Protein folding is a carefully regulated process that is determined at its core by the amino acids in the chain: their hydrophobicity and hydrophilicity and how they interact together.

In many instances, however, a complete protein consists of more than one amino acid chain, and the complete protein has two or more interacting strings of amino acids. A good example is hemoglobin in red blood cells. Its job is to grab oxygen and deliver it to the body’s tissues. A complete hemoglobin protein consists of four separate amino acid chains all properly folded into their tertiary structures and interacting as a single unit. In cases like this involving two or more interacting amino acid chains, we say that the final protein has a quaternary structure. Some proteins can consist of as many as a dozen interacting chains, behaving as a single protein unit.

A Plethora of Purposes

What does a protein do? Let us count the ways. Really, that’s almost impossible because proteins do just about everything. Some of them tag things. Some of them destroy things. Some of them protect. Some mark cells as “self.” Some serve as structural materials, while others are highways or motors. They aid in communication, they operate as signaling molecules, they transfer molecules and cut them up, they interact with each other in complex, interrelated pathways to build things up and break things down. They regulate genes and package DNA, and they regulate and package each other.

As described above, proteins are the final folded arrangement of a string of amino acids. One way we obtain these building blocks for the millions of proteins our bodies make is through our diet. You may hear about foods that are high in protein or people eating high-protein diets to build muscle. When we take in those proteins, we can break them apart and use the amino acids that make them up to build proteins of our own.

Nucleic Acids

How does a cell know which proteins to make? It has a code for building them, one that is especially guarded in a cellular vault in our cells called the nucleus. This code is deoxyribonucleic acid, or DNA. The cell makes a copy of this code and send it out to specialized structures that read it and build proteins based on what they read. As with any code, a typo–a mutation–can result in a message that doesn’t make as much sense. When the code gets changed, sometimes, the protein that the cell builds using that code will be changed, too.

Biohazard!The names associated with nucleic acids can be confusing because they all start with nucle-. It may seem obvious or easy now, but a brain freeze on a test could mix you up. You need to fix in your mind that the shorter term (10 letters, four syllables), nucleotide, refers to the smaller molecule, the three-part building block. The longer term (12 characters, including the space, and five syllables), nucleic acid, which is inherent in the names DNA and RNA, designates the big, long molecule.

DNA vs. RNA: A Matter of Structure

DNA and its nucleic acid cousin, ribonucleic acid, or RNA, are both made of the same kinds of building blocks. These building blocks are called nucleotides. Each nucleotide consists of three parts: a sugar (ribose for RNA and deoxyribose for DNA), a phosphate, and a nitrogenous base. In DNA, every nucleotide has identical sugars and phosphates, and in RNA, the sugar and phosphate are also the same for every nucleotide.

So what’s different? The nitrogenous bases. DNA has a set of four to use as its coding alphabet. These are the purines, adenine and guanine, and the pyrimidines, thymine and cytosine. The nucleotides are abbreviated by their initial letters as A, G, T, and C. From variations in the arrangement and number of these four molecules, all of the diversity of life arises. Just four different types of the nucleotide building blocks, and we have you, bacteria, wombats, and blue whales.

RNA is also basic at its core, consisting of only four different nucleotides. In fact, it uses three of the same nitrogenous bases as DNA–A, G, and C–but it substitutes a base called uracil (U) where DNA uses thymine. Uracil is a pyrimidine.

DNA vs. RNA: Function Wars

An interesting thing about the nitrogenous bases of the nucleotides is that they pair with each other, using hydrogen bonds, in a predictable way. An adenine will almost always bond with a thymine in DNA or a uracil in RNA, and cytosine and guanine will almost always bond with each other. This pairing capacity allows the cell to use a sequence of DNA and build either a new DNA sequence, using the old one as a template, or build an RNA sequence to make a copy of the DNA.

These two different uses of A-T/U and C-G base pairing serve two different purposes. DNA is copied into DNA usually when a cell is preparing to divide and needs two complete sets of DNA for the new cells. DNA is copied into RNA when the cell needs to send the code out of the vault so proteins can be built. The DNA stays safely where it belongs.

RNA is really a nucleic acid jack-of-all-trades. It not only serves as the copy of the DNA but also is the main component of the two types of cellular workers that read that copy and build proteins from it. At one point in this process, the three types of RNA come together in protein assembly to make sure the job is done right.

Jeffrey, a recovering scientist, has always had a passionfor the technology and the gadgetry of science. He has been ascientific writer and editor since 2000, when he left academia to jointhe staff of The Scientist magazine as a Senior Editor for Technology.Before that, he studied transcription factor biology at the Universityof Pennsylvania and Harvard Medical School -- training that,surprisingly, has little application in the real world. In 2006, heand his family headed west to Pocatello, Idaho, and has been afreelance writer ever since. You can see why Double X Science is thrilled to have him on the team! You can find Jeffrey at his Website or on Twitter at @j_perkel. Welcome, Jeff!]

It alarmed me because, well, I don’t like microbes much (despite, or perhaps because of my background in microbiology), and this article is about people getting very, very sick from sepsis (aka septicemia or bacteremia, an infection of the blood), which presents itself as a whole-body inflammatory response and a significantly increased risk of organ failure. It is an important area of microbiology because sepsis results from a bacterial infection, and the article says that 20% to 50% of infected patients die from sepsis.

My interest was piqued, however, because the piece goes on to talk about how a new genetic testing device that the US Food and Drug Administration approved in June could possibly help rein in the disease. That’s because it can reduce the time for diagnosing sepsis from days to hours. And when it comes to sepsis, time is critical.

Sepsis is confirmed by testing for the presence of specific types of bacteria in blood samples from patients and identifying what bacteria, if any, are in the circulation. If they are present, the researchers need to find out if the bugs are resistant to any antibiotic. Unfortunately, all that takes time – time the patient often doesn’t have. As the news story notes,

About the size of a small microwave oven, the Verigene Gram-positive Blood Culture Nucleic Acid Test is the first system approved by the FDA to identify quickly certain bacteria responsible for bloodstream infections — and whether some are resistant to the top drugs used against them.

Instead of the three days required for a traditional blood culture panel, results from the Verigene test come back within three hours, identifying up to a dozen specific bacteria known to cause sepsis, including strains of Staphylococcus, Streptococcus, Enterococcus and Listeria.

Of particular importance, the system can catch some particularly nasty bugs, methicillin-resistant Staphylococcus aureus (MRSA; see Maryn McKenna’s excellent Superbugif you really want to terrify yourself on this subject) and vancomycin-resistant Enterococci.

In its press release announcing the Verigene test’s approval, the FDA said that, compared to standard microbiology methods, the Verigene test results “were consistent with traditional blood culture methods in 93 percent to 100 percent of the comparisons.”

The test is remarkably simple, and even automated, requiring a dedicated sample processing instrument and a reader from Nanosphere.

The patient sample is added to a glass slide covered with capture signals that recognize DNA from sepsis-causing bacteria. The capture signals are placed on the glass slide in a defined order, each programmed to recognize only one strain of bacteria. This uniform order helps scientists identify which strain of bacteria, if any, is responsible for the infection. If the patient blood sample contains bacteria, the signals on the glass slide will capture its DNA, and the special scanner and software can detect this capture.

What sets the Verigene test apart from the previously available tests for sepsis is precisely how they do the detecting. The test adds sub-microscopic gold balls, called gold nanoparticles, to the glass slide. These gold nanoparticles are studded with more capture signals. When bacteria match up with the same specific capture signals, the nanoparticles will attach to that area. This ball gives scientists the ability to more rapidly detect which type of bacteria, if any, is present, and thus select the right course of antibiotic treatment.

The reaction is developed by coating the gold nanoparticles with silver, a process called signal amplification, which increases sensitivity up to 100,000 times, and then hitting it with light. Those spots containing the nanoparticles scatter light; those without it, do not. The effect is so strong, the original paper detected it using a “conventional flatbed scanner,” like something you’d have in your home office.

According to Nanosphere’s website, the whole thing requires less than five minutes’ worth of hands-on time, plus 2.5 hours to get the result. That falls within the necessary time frame to diagnose sepsis and begin life-saving antibiotic therapy.

Hopefully, this is a technology that neither your family nor mine will ever need. But it’s nice to know it’s there. And now, you know how it works.

(If you’re interested in the research paper that led to this test, from company cofounders Robert Letsinger and Chad Mirkin, both of Northwestern University, you can read it here.)

Jennifer Canale is a Senior Microbiologist for the United States Food and Drug Administration (FDA) in Queens, NY, as well as an adjunct microbiology lecturer for City University of NY (York College and College of Staten Island). Jennifer is also passionate about promoting women in science and leads an annual women in science event at the FDA as a means to promote awareness about gender discrimination in the workplace.[DXS] First, can you give me a quick overview of what your scientific background is and your current connection to science?

[JC] I have always been interested in science, and since most of my family worked in Bellvue Hospital, I was very comfortable around people in lab coats. In the early seventies, at the age of 5, I announced to my grandfather, the X-ray technician, and his brothers (my great uncles) that I wanted to become a doctor, specifically a doctor that delivers babies.

My grandfather was proud and my uncles were dismayed. My uncle Joe said to me, “Jennifer, you mean a nurse like your cousin Joanie, right?” My cousin Joan applied to Medical School in the sixties and the same group of uncles convinced her that her fiancé, Warren, wouldn’t wait 4 years to get married and it was more lady-like to be a nurse. Today she is a retired left-handed OR nurse that specializes in cracking open chests for cardiac surgery, not so lady-like after all. So in an attempt to not have a repeat of Joanie, my grandfather jumped to my defense against his brothers and said that ‘she can be a doctor if she wanted to be’, and, furthermore, his niece Joanie was smarter and more capable than most of the doctors he worked with and shouldn’t have had to take orders from them.

My uncles agreed that there was no question of the intellectual prowess possessed by both Joanie and myself, and their reluctance came out of concern for me. They worked in the hospital, too, and saw how male doctors would abuse the female ones and make their lives more difficult because they didn’t want to allow girls in the all-boys club. “Do you want our baby – our most precious blood – to have to fight her whole life for this? What about the family – how will she find a husband and bring us more children if she sticks her nose in a book the rest of her life?” These arguments sounded a lot better when they were stated in Sicilian. Back then, the concept of ‘women can have it all’ – work and family – was not the norm like it is today.

My grandfather came back with his final answers to them. I was his granddaughter, I looked just like him, I was a fighter just like him, and this is America and she will be what she wants to be, ‘End of Story’. My uncles agreed that I was his granddaughter, I looked just like him, and I was a stubborn mule just like him, so he was probably right and they would pray for me and secretly hope I would change my mind.

Now this all transpired in front of me in a combination of English and Sicilian while I stood there in my denim overalls with a Tweety Bird patch. I was listening, and since I was only beginning to learn Sicilian, I only caught a couple of words: blood, children, book, change, and I misunderstood the word for fighter as “afraid.” I added to my grandfather’s “end of story” remark that I was not afraid of blood, I can learn how to deliver children from a book, and questioned why they wanted me to change- those overalls were my favorite!

My family was supportive to a point, but when I asked for an erector set for Christmas, I got a Barbie town house. When I wanted to go camping with the Girl Scouts, I was sent to dance school (but, much to my amazement, I enjoyed that until I was 17). My parents started giving in around 3rdgrade, and I got the panda bear-shaped calculator I wanted, as well as the robot toy 2XL featuring the 8-track tape. My mom would beg me to watch Little House On the Prairie, but I preferred Star Trek (the original Kirk version), Lost in Space (Danger Will Robinson), and Land of the Lost. Of course this was all my dad’s fault according to mom – he was the sci-fi guy, but he always said, “Jen was born this way!”

My parents eventually gave up, and my uncles kept praying for that change of mind, but I spent the late seventies and early eighties winning science fairs with experiments my Uncle Ben, the electrician, rigged for me. They thought there was hope for me to be more “lady-like” in 1984 when I started high school and wanted to try out for the cheerleading squad, but the teachers advised me that “the cheer squad” was no place for an “honor student” like me. So it was off to advanced placement Biology and Chemistry, and by graduation in 1988, I was accepted to the pre-med program at NYU.

I graduated from NYU with honors, and my parents got me two presents: my name in diamonds and a stethoscope. My grandfather bought me a set of crisp white lab coats and gloated to his brothers with a cigar in his mouth. Apparently a bet was made amongst them and from hence forward they had to call me “doctoressa,” the hybrid feminized version of doctor in Italian.

The NYU pre-med was highly competitive – a constant process of elimination from 500 students (1:3, female:male) down to only 109 of us actually completing the program. The men thought it was strategic to flirt with the girls and convince us that we shouldn’t become doctors but instead should marry them. The guy that told me that got a punch in the stomach – in the name of the other women that worked. It was also apparent that many were planting the seeds of doubt in the pre-med females, stating that if we became doctors, then we wouldn’t be able to have a family. In essence, we were being told that we would be giving up the chance to have children. You had to go against your “true female nature” to breed and nurture and (instead) become a selfish and testosterone-like human to make it in this field. That was the nail in the coffin for a lot of the women in my program. The most brutal tactic and final blow to confidence was when I heard someone say that “only the ugly girls become doctors because no man would want them.”

In the nineties – halfway through college – I did change my mind, and my uncles were dancing in the streets. They thought I met a nice boy in college and I was going to settle down, give them more kids, and make sauce and meatballs on a Sunday like the good Paesana I was supposed to be. I announced I didn’t want to be an MD anymore, I wanted to be a PhD, instead. I wanted to be a SCIENTIST, do research, and maybe teach in a university. A “Scientista”-“Professoressa” “Aiuta Dio” (which means help us god)! Back to church and the rosary beads. When I got my master’s degree in microbiology, the family was just convinced I liked to collect graduation hats.

There was a feeling among my family members that science was a “boy thing,” and my cousins teased me as a result. They considered me a nerd and less feminine than my other girl cousins. I was told that I would never get married and have kids because I am a bookworm. Even in the mid-’90s, I had friends that told me not to tell guys that I was a scientist because they wouldn’t ask me out. I was kind of cute and only told a guy the truth about my profession if we got serious. As an experiment, I told one guy I met that I was a scientist and he said I looked too sexy to be that smart – and then he walked away.

I met discrimination on both sides of the stereotypical coin, in academia and in the work force. I was told when I was interviewing for graduate schools (and then for science jobs) that I had several strikes against me. First, strike one, my thick Staten Island/ Brooklyn accent supposedly made me sound less intelligent. My mentor in graduate school, Dr. Mark Albano, said to tell people to kiss your “you know what” because as long as I could discuss topics like “molecular genetics” who cares how it sounds. Besides he found my accent endearing, especially because it made boring topics sound more interesting.

Strike two was my long hair. I was told that my long hair was not practical in a scientific environment, and if I looked too glamorous on interviews I would not be taken seriously. I put my hair in a bun and toned down my make-up, but I didn’t cut it. Apparently, I looked too feminine, especially given my major curves, and even my power suits could not hide that. Women at the time were dressing very masculine (think early Miranda on Sex in the City) to compete with men for jobs. When I got the interview for my first job with Dr. Moretti in the Reproductive Immunology Lab at St. Vincent’s Medical Center in Staten Island, I remember wearing a black and white houndstooth print sheath dress with a matching short suit jacket, accessorized with pearls. Dr. Moretti said I was like Rosalind Franklin and Jackie Kennedy all rolled up into one, with a side order of cannoli.

The early 2000s arrived, and attitudes toward science changed. Shows like CSI became wildly popular. Science fiction movies about transforming robots became blockbusters. People began to use technology in their everyday lives, such as smart phones, tablets, and car navigation systems, and it suddenly became “cool.” I met my husband in 1999, and since I really was into him, I told him the truth about being a “microbiologist” from the start. He said, and I quote, “Wow, your smart, sexy, and Sicilian – it’s like I hit the Lotto!”

My wedding was the most joyful event in our family’s history because most of them thought that would never happen. I still get teased by my family when I give a long, drawn out scientific explanation of something or when I bake and make exact measurements of ingredients with my Pyrex bakeware with both the ounces and metric conversions. My husband responds for me and says “he learns something new everyday and hopes that our son becomes a nerd just like his mommy.”

So now I have it all: I am a female scientist, a wife, and a mother, even though others didn’t think that would be possible. But I always knew it would happen. I understood and forgave my uncles because I knew that they wanted to protect me, not hinder me. As for all my doubters I regularly take Dr. Albano’s advise and tell them to kiss my “you know what!”

Even my current supervisor, Maureen Coakley, recently told me in an interview that I am an “anomaly,” meaning that I am a flamboyant scientist. That was one of the best compliments I ever received. I am who I am, and that is why my playlist on my iPhone has the “Big Bang Theory Theme Song” followed by “I’m sexy and I know it!”

Times have changed. Perceptions have altered in a good way, but not entirely. Lesson learned from both academia and the school of life is that some people will get you and some people won’t. If they don’t, don’t take it personally because it is their loss and their ignorance. Some people see the person, and some see the stereotype. All you can do is try to educate them in an attempt to bust the stereotype. The only perception that matters is how you perceive yourself and use that perception as a means to become the woman that you were meant to be.

[DXS] What ways do you express yourself creatively that may not have a single thing to do with science?

[JC]Ever since planning my wedding in 2004, I have been interested in event planning. I have a knack at coordinating events, which I do as part of my collateral duties at FDA, where I have served as the Women’s Program Coordinator for the past 9 years. People call me the ”Fun Fairy” because I can be very creative and take any topic, put a different and interesting spin on it, and present it to a group in very entertaining ways. My creativity is driven by my intellectualism, and I incorporate that into something fun and memorable. I always make little inexpensive favors – buy them to give out to my audience – that are”theme oriented,” and they keep them as a reminder of the event.

The people I work with have whole collections of these favors, and they remember what each one stands for. For instance, the Women’s History Month theme for one year was “Our History is Our Strength.” Before planning this event, I had attended at NYU the Satellite Summit of National Women’s Conference hosted by Maria Shriver (then 1st Lady of California) and the First Lady, Michelle Obama. So I thought I would highlight the contributions of the First Ladies to US history. I found an educational video on the history of the First Ladies, did a presentation on the Satellite Summit, and even had a fashion show featuring of reproductions of Jacqueline Kennedy jewelry collection (my favorite first lady). I used the symbol of a “Cameo” to represent the first ladies, and so I made a huge paper one with beads on tulle on my bulletin board with pictures of the first ladies around it and gave out cameo bracelets that I made from gluing plastic cameo buttons on ribbon. Everyone still has a cameo on their desk at work, occasionally conjuring up memories of my First Ladies event.

[DXS] Do you find that your scientific background informs your creativity, even though what you do may not specifically be scientific?

[JC]My entire life is influenced by, or even revolves around, “Science.” I love science fiction movies, books, comic books, etc. Any inspiration I get for any of my creative projects always has some root in something “science-related.” I also think that my background in science helps make my visions come to life. Even the smallest details like the stemware I chose for my wedding was a Mikasa pattern that resembled a DNA double helix, or a hexagonal candleholder that looked like a benzene ring (at least it did to me!). Another example comes from my Women’s Program, when the theme was “Writing Women Back Into History.” So I found a book called The Women of Apollo, which gave the untold story of the women engineers who had critical contributions to the Apollo Space programs. For me, all roads lead back to science.

[DXS] Have you encountered situations in which your expression of yourself outside the bounds of science has led to people viewing you differently–either more positively or more negatively?

[JC]I have experienced both negative and positive views by others when I am expressing my self creatively. On one hand, there were people that associate planning events with a negative stereotype of being a “party-girl” or “bimbo” type that cares more about the “girly fun” stuff than the serious business of science. On the other hand, there have been people who constantly praise me for presenting science-related topics in entertaining ways. The latter view me as a “flamboyant scientist” who shares her knowledge in an interesting manner. In this life you will never please everyone; only seek to please yourself and your loved ones because those are the only opinions that matter.

[DXS] Have you found that your non-science expression of creativity/activity/etc. has in any way informed your understanding of science or how you may talk about it or present it to others?

[JC]In planning these events, I have come up with a formula of sorts to create a successful soirée. Of course, this formula is an entire science in itself. I have to consider things like timing, lighting, printed materials (programs, table cards, menus, etc.) and a gamut of other things that involve an understanding of science. I am a biologist with a minor in chemistry, but the more I do these events, the more I get into things like astronomy (for a celestial-themed wedding, for instance). I mention lighting, which seems so simple, because it is actually quite complicated – getting the right reflections and materials to use (i.e.- LEDs, wax candles vs. battery operated, the limitations of pyrotechnics in party venues) is critical. Even in doing crafts for favors and printed materials, like event programs, I’ve learned different scientific techniques, such the right kind of bonding agent to use to attach ribbons, charms, or vinyl decorations, or even the use of edible ink in printers to make fondant or wafer decorations to put on cupcakes or cakes. It is a continuous learning experience.

[DXS] How comfortable are you expressing your femininity and in what ways? How does this expression influence people’s perception of you in, say, a scientifically oriented context?

[JC]I am comfortable with expressing my femininity in the way I dress and conduct myself in any setting. Although, many years ago, I was advised to dress in suits and tailored shirts similar to a man and wear neutral make-up or none at all if I wanted to be taken seriously in the scientific world, I went against the grain. I am a curvy girl, and there is no hiding my femininity. So I embrace it. I wore suits, but nothing drab – always something like a red or purple skirt suit with heels. I adhere to work environment rules like no open toe shoes in the lab, which is a safety concern, but I do not downplay my female attributes to fit in, or to present a more palatable image to my scientific peers. I do not concern myself with people’s perceptions of me based on my looks because once I “speak” and “communicate” scientific concepts, there is no question of my prowess. I am what I am, and that is a female scientist, and I pride myself in being a “stereotype buster.”

[DXS] Do you think that the combination of your non-science creativity and scientific-related activity shifts people’s perspectives or ideas about what a scientist or science communicator is? If you’re aware of such an influence, in what way, if any, do you use it to (for example) reach a different corner of your audience or present science in a different sort of way?

[JC]I think that being the “flamboyant scientist” works in my favor, and as a science communicator, it is effective all aspects of my life. As an adjunct professor, my students often thank me for making science fun and understandable. As a scientist, my colleagues and interns find my training methods to be memorable and actually increase their understanding of the job. As the Women’s Program Coordinator at the FDA, I create unforgettable events that people look forward to and learn a lot from. As a wife, mother, daughter, aunt, cousin, and friend, I am the “Fun Fairy” (pictured with wings and a lab coat), and their lovable nerdy girl.

I feel my true gift is being able to communicate science. My mentor in graduate school always told me I had the talent of taking complicated scientific ideas and expressing them in a way that anyone could understand. I have some ideas brewing involving science books for children and teens, and I would like to explore these avenues in order to share this gift with others. I would also like to get involved in maybe writing for popular science publications, if given the opportunity.

[DXS] If you had something you could say to the younger you about the role of expression and creativity in your chosen career path, what would you say?

[JC]I would say be true to yourself. Whatever path you take career-wise, always remember that is could be something you will be doing the rest of your life. Yes, there are financial considerations to make, but if you do not have that creative outlet incorporated into your career, then you will be miserable. I am the happiest at work when I am planning a Women’s Program alongside doing experiments or going to my second job as a professor at York College. You need the creativity to keep the blood flowing. Where would science be without creativity? Find what your talent is and what makes you happy, and then apply it to your career. That is the secret to success.

Back when I taught college general biology, I always gave a lecture in which we talked about ecosystems. At the beginning of the lecture, I showed them the above image or a similar one and explained that the handsome organism it features lives quietly and unobtrusively in the hair follicles on your face. My goal was to combine horror and information so that my students would never forget that they, too, are ecosystems–and, I hoped–get acclimated to the idea. Most of them just seemed pretty creeped out.

The animal above is a mite and member of the Demodex genus. Because of its affinity for follicles, it’s known as Demodex folliculorum. Its partner in existence on your face (and some other places) is the shorter version, known as Demodex brevis [PDF], which is drawn to your sebaceous (oil) glands, also on your face. Because they have “piercing-sucking mouth parts,” pedipalps, and eight legs in four pairs, according to one lovingly detailed description in a 1976 paper, they are arachnids, just like spiders. Tiny arachnids that live on your face, taking moonlit strolls when it’s dark and diving for cover in light. They live there, just as you live in a house, except your face is like an array of microscopic cave houses where these organisms reproduce and eat. And apparently are rather active; from a 1985 paper about these mites and what they do on your eyelids:

The normally torpid existence of demodectic mites of the eyelid changes with the onset of oviposition (egg laying). There occurs a burst of activity characterized by flexion, extension, and rotation.

In addition to all of flexing and extending and rotating, these mites also happen to die on your face. They “disgorge” products from their salivary glands while alive, but when dead, they appear to disintegrate, releasing the contents of their guts onto you and the visage you show the world. As it happens, the mites themselves are, like you, hosts to unseen organisms, in this case the bacteria in their guts.

The word on the street–and in this paywalled paper–is that these mites don’t have anuses. Thus, after suffering from a near-lifelong (a few days at most) case of constipation, they die and unconstipate all over you.

If the idea of dead mites reproducing and dying and disintegrating all over your face didn’t do you in, congratulations. You’re a rational person resigned to your inevitable fate as an ecosystem. Either way, you may have wondered: What does this mite-y fecal matter do to my face?

Experts have disagreed about what these mites and their, er, exudants do to their host, but studies have found links between their presence and abundance and several dermatological and other diseases. Among these, rosacea is possibly the best known, in part because it is relatively common (up to 3% of people worldwide have it) and easy to spot: It produces a pronounced redness of the skin, sometimes with a sandpapery look, and with age and as it worsens, can result in manifestations like bumps on the skin and gritty eyes, including effects on the nose like those in this painting:

A nose with features of end-stage rosacea (left).Public domain, via Wikimedia Commons.

Indeed, as we age, the population of these mites grows, and rosacea is considered a chronic condition that crops up most often between the ages of 30 and 50 or 60. It also has had an air of mystery about it, including why some people develop it and others do not, and what, exactly, causes it. Now, researchers who have conducted a deep review of all of the rosacea-related research suggest that it’s primarily a bacterial infection. The source of the bacteria? That mite poop.

Does that mean that people who don’t have rosacea are in some way less fecally affected than people who do? Not necessarily. These mites are “commonly” found on people without any outward manifestation of effect. But people with rosacea may develop it thanks to wonky immune systems that underreact or overreact to the mites or the bacteria in their poop, according to the authors of the review, published in the Journal of Medical Microbiology.

In other words, people who have rosacea might actually be fighting the mites and their poop contents harder than people without it, so no need to feel all superior if you’re rosacea free. Rosacea is more common in women than in men, which is in keeping with a general female prevalence of disorders of immune wonkiness. Also, just in case menopause didn’t carry enough baggage, rosacea happens to strike women “particularly” during that time our ovaries are saying their sayonaras.

One of the bacteria in question actually might begin as just another resident lurking in the ecosystem that is your skin. The mites eat the bacteria along with the delicious (I’m assuming) skin cells they consume. When the mites die and disintegrate, bacterial bits may emerge along with other components of the mite digestive contents. It is possible, say the review authors, that these bacterial bits–like lots of other bacterial bits–trigger an immune response that we see as rosacea. Indeed, one antibiotic, doxycycline, that’s particularly well known for conquering this bacterium, is reasonably effective for rosacea.

What can you or any of us do to prevent or treat rosacea? As far as prevention, the review authors note that in some cases, a genetic immune wonkiness may predispose some people to developing it. Because these mites often are deeper than skin surface, techniques like exfoliation are unlikely to be helpful. As science writer Ed Yong cautions in his fantastic piece about this review paper, do not try to bleach your face, either. Current treatment consists of a topical medication to reduce inflammation and oral antibiotics. In severe cases, a medication used for cystic acne and that actually inhibits sebaceous gland secretion is a possibility.

Do you or does someone you know have rosacea? What treatments have you tried? Given the potential involvement of a wonky immune system, have you noted any co-occurrence of other immune-related problems?